1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).
It took a while but it’s finally published!
The GAP activity of SEAC (GATOR) is a metabolic switch that allows cells to quickly respond to changes in amino acid levels, both for inhibition and reactivation.
🚀 CryoSPARC v5.0 BETA is here!
We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread!
Full changelog: cryosparc.com/updates/v5.0.0
CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!
Structures from AlphaFold3 - while often impressively good - tend to fail representing the dynamic ensembles accurately. And often parts of the structure are not correct. Adding experimental data, directly in AlphaFold's diffusion step, provides physically realistic protein ensembles. This image shows two cases where AlphaFold3-only structures were largely improved by guiding with experimental data.
📢 New preprint:
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
Just tried your HR-HAIR + local refinement pipeline (with tweaked settings based on the pre-print) on a dataset of a small protein complex which did not result in any decent ab-initio reconstructions. HR-HAIR took 19 hours, but damn, result is insane! Many thanks!
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
This is fantastic!! Very nice work!
And additionally, many thanks to Wouter Van Putte @pxn001.bsky.social (PUXANO) for providing their fantastic graphene-coated EM grids!!!
Congrats to everyone involved at Sophie Lucas Lab (especially Blueskyless co-first authors Fanny Lambert and Séverine Wautier), @argenx.com and @savvideslab.bsky.social at @viblifesciences.bsky.social!
Now published @cp-cellreports.bsky.social! Antibody-mediated TGF-β1 activation for the treatment of diseases caused by deleterious T cell activity: www.cell.com/cell-reports...
Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.
We are excited to announce the first in-cell structure of a LINC complex within a native nuclear envelope at subnanometer resolution!! #In-cell cryo-ET + #atomistic MD simulations! @tomdendooven.bsky.social et al!!
www.biorxiv.org/content/10.1...
Thanks Piotr!
Finally out @natcomms.nature.com
"Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses".
Great collab between @savvideslab.bsky.social (we performed #CryoEM) and Xavier Saelens Lab, spearheaded by Arne Matthys.
www.nature.com/articles/s41...
If this is true, it’s abysmally shortsighted for #NIH. The new tools nurtured by the long series of #CASP challenges probably contribute far more in one year to the scientific and industrial economies than the entire funds that have supported it.
We have a preprint for you
EHD2 forms rings on caveolae necks, in contrast to most EHDs forming helices. We determined its structure on membranes and show that N-term acts as a spacer
By Elena, Vasya @vasiliimikirtumov.bsky.social, Jeff &Oli Daumke www.biorxiv.org/content/10.1...
I’m very happy to share my first paper on the effects of AWI interactions and flexibility on SPA data quality! Thank you to everyone on the team 🤩
www.sciencedirect.com/science/arti...
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Reanalysis of cryo-EM data from EMPIAR entry EMPIAR-10,930 deposited by Reshetnyak and colleagues, Nature (2021). (A) Ten most populated 2D class averages after performing 2D classification on 11.8 million selected particles. Classes corresponding to 2:1 ALK–ALKAL2 particles are highlighted in blue, while classes corresponding to 2:2 ALK–ALKAL2 particles are highlighted in orange. (B) Ab initio model generation in cryoSPARC results in classes corresponding to both a 2:1 ALK–ALKAL2 and 2:2 ALK–ALKAL2 assembly. Hetero-refinement of the 2:1 and 2:2 ALK–ALKAL2 classes results in the two models displaying 2:1 and 2:2 ALK–ALKAL2 assemblies, respectively. The ALK–ALKAL2 complexes with 2:1 (PDB 7nwz) and 2:2 (PDB 7n00) stoichiometries are shown fitted inside the maps, with ALK colored pink/gray and ALKAL2 colored blue/purple. (C) 3D refinement; a front view is shown of a map sharpened in RELION using a B-factor of −100 Å2, with ALK colored pink/gray and ALKAL2 colored blue. Front, side, and top views are shown of a transparent map, sharpened using deepEMhancer, with fitted structural model.
Reports of diverse stoichiometries have complicated our understanding of the complex between ALK kinase and its #cytokine ligand ALKAL2. @janfelix.bsky.social @savvideslab.bsky.social &co reanalyze #cryoEM data to clarify the situation @plosbiology.org 🧪 plos.io/4lvRfvu
Delighted to share our reanalysis of cryo-EM data in EMPIAR-10930, now at:
journals.plos.org/plosbiology/... ;
revealing the ALK-ALKAL2 assembly with 2:1 stoichiometry and resolving the conundrum introduced by the originally reported 2:2 complex. ALK/LTK-cytokine signalling getting clearer!
#CryoSPARC v4.7 is out! 🚀
Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more!
Full changelog: cryosparc.com/updates
#cryoEM
I'm super happy that our story is now published!
📖 www.science.org/doi/10.1126/...
But what changed compared to the original preprint?
Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.
Foam film vitrification for cryo-EM www.biorxiv.org/content/10.1101/2025.03....
Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.
New preprint from the @remaut-lab.bsky.social ! Happy to share our latest work on a new member of the ENA family, protein fibers found on the spore’s surface. Using CryoID @mikesleutel.bsky.social identified F-ENA in BTK. The paper dives deep into its structure analysis by integrating X-ray and AF3
Cryo-EM structures of mammalian membrane proteins from a single cell culture dish?
Yes, Micro ISOlation (MISO) sample preparation makes it possible.
www.biorxiv.org/content/10.1...
Happy to be part of this exciting story and wonderful collaboration with the Rouslan Efremov lab.
It is definitely a pseudo symmetry case (symmetric dimeric receptor assembly with asymmetric ligand in between). I did not try your suggested workflow. For this particular case 3D orientation rebalancing + BLUSH combo did the trick and results in a nice 3ish Å map from severely anisotropic data.
To correct my previous post: the map is already deposited to the EMDB, I meant to put the .star file corresponding to the new map on EMPIAR.
